Initiation of DNA replication by DNA polymerases from primers forming a triple helix.

Despite extensive studies on oligonucleotide-forming triple helices, which were discovered in 1957, their possible relevance in the initiation of DNA replication remains unknown. Using sequences forming triple helices, we have developed a DNA polymerisation assay by using hairpin DNA templates with a 3' dideoxynucleotide end and an unpaired 5'-end extension to be replicated. The T7 DNA polymerase successfully elongated nucleotides to the expected size of the template from the primers forming triple helices composed of 9-14 deoxyguanosine-rich residues. The triple helix-forming primer required for this reaction has to be oriented parallel to the homologous sequence of the hairpin DNA template. Substitution of the deoxyguanosine residues by N7 deazadeoxyguanosines in the hairpin of the template prevented primer elongation, suggesting that the formation of a triple helix is a prerequisite for primer elongation. Furthermore, DNA sequencing could be achieved with the hairpin template through partial elongation of the third DNA strand forming primer. The T4 DNA polymerase and the Klenow fragment of DNA polymerase I provided similar DNA elongation to the T7 polymerase-thioredoxin complex. On the basis of published crystallographic data, we show that the third DNA strand primer fits within the catalytic centre of the T7 DNA polymerase, thus underlying this new property of several DNA polymerases which may be relevant to genome rearrangements and to the evolution of the genetic apparatus, namely the DNA structure and replication processes.

Expression of E. coli RecA targeted to mitochondria of human cells.

Mitochondrial DNA integrity is ensured by several nuclear-encoded proteins in vertebrates, and a number of mtDNA alterations in human diseases, including deletions and duplications, have been suspected to result from errors in the mitochondrial recombination pathway. However, the presence of the latter system is still a matter of controversy as RecA proteins display various functions in vitro. In Escherichia coli, RecA plays a central role in homologous recombination by pairing and transferring a single strand to a homologous duplex DNA. To address indirectly the issue of a mitochondrial recombination pathway in vivo, we have constructed a chimeric gene containing an N terminal mitochondrial targeting sequence and the E. coli RecA gene. Cells were transfected by the recombinant plasmid, then tested for their mtDNA repair upon bleomycin treatment. We found an increased repair rate of the mitochondrial DNA in cells expressing RecA as compared to control cells. These results indicate that the transfected cells display an improved mtDNA repair replication pathway due to the exogenous RecA, likely in synergy with an endogenous rate-limiting mitochondrial recombination pathway.

Oligoasthenospermia associated with multiple mitochondrial DNA rearrangements.

A patient who wished to be treated for infertility by intracytoplasmic sperm injection (ICSI) was referred to our group for assessment. Upon clinical examination, a ptosis (partial closure of the eyelid) was noted, and histology revealed ragged red fibres in the skeletal muscle. Southern blot analysis of spermatozoa and skeletal muscle revealed the presence of multiple mitochondrial DNA deletions. This kind of rearrangement may be of nuclear origin since three nuclear loci have been ascribed to multiple mitochondrial DNA deletions in humans. Since mitochondrial DNA is maternally transmitted, the use of ICSI was feasible. However, an alteration of nuclear gene product affecting the integrity of mitochondrial DNA, and thus sperm mobility, might be transmitted to the offspring with the risk of developing a mitochondrial DNA disease.

Male infertility associated with multiple mitochondrial DNA rearrangements.

Male sterility results from a number of characterized exogenous or genetic dysfunctions preventing normal differentiation into mobile spermatozoa. This may now be overcome by intra cytoplasmic sperm injection (ICSI). This practice does not require mobile, or even mature spermatozoa for in vitro fecondation. However, a functional respiratory chain, partly encoded by the mitochondrial DNA (mtDNA), is required for the mobility of the spermatozoa. We report the case of an infertile patient who wished to procreate. ICSI was proposed but he displayed multiple mtDNA deletions of possible nuclear origin in the spermatozoa and in the deltoid muscle. Even though mtDNA is maternally inherited, the possibility of a nuclear-driven mutation affecting the integrity of the mtDNA should be taken into account when ICSI is to be performed. Together with recent genetic in vitro manipulations in mammals, our data point to the importance of studying the mtDNA structure in human spermatozoa, and the potential risks of these non-natural practices for procreation.

[Do mitochondria play a role in aging?]. / Les mitochondries jouent-elles un rôle dans le vieillissement?

Ageing is an unavoidable and complex phenomenon which may be a price to pay to evolution. Thus genetics appear to play a predominant role besides environmental factors. Energetic metabolism slowly declines with ageing supporting a possible active role of mitochondria, the power supply of the cells, to this process. Mitochondrial DNA alterations appear during the mid-life and in degenerative diseases such as in Parkinson's and Alzheimer's; they include large scale deletions and point mutations. Since the respiratory chain plays a major role in the generation of superoxide anions which are converted into hydroxyl radicals that may impair lipids, proteins and DNA function in mitochondria, this vicious cycle may result from both an altered control of mitochondrial biogenesis dependent from the nucleus, and/or from a lack of repair and accumulation of somatic mitochondrial DNA mutations.

Role of the mitochondrial DNA and calmitine in myopathies.

We present data on mitochondrial DNA deletions and mitochondrial diseases. The mechanism of their occurrence is discussed on the basis of deletion breakpoints and particularly with the slippage mispairing hypothesis. As the correlation between the genotypes and the phenotypes is not always straightforward, a classification of mitochondrial diseases is suggested according to the genotype (deletions, depletions and duplications, mutations affecting structural genes or tRNA genes) rather than the phenotype. The effect of mitochondrial DNA alterations on the expression of nuclear encoded proteins is presented, and the nucleus can be found to respond differently but in a coordinate way according to the kind of mitochondrial DNA alteration. The search for a nuclear gene affecting the expression of Leber's disease could not show any correlation between the alleles of TAP2 (transporter antigen peptide) and the expression of the disease. Finally, we present new data on another class of myopathies, namely Duchenne muscular dystrophy (DMD), where mitochondria could play an unexpected role in the metabolism of calcium. In some patients with DMD a mitochondrial calcium binding protein that is mainly located in the mitochondrial matrix and which is named 'calmitine' was found to disappear. We have thus cloned its cDNA and found that it was identical with to calsequestrine which is a high-capacity but low-affinity Ca2+ binding protein from the sarcoplasmic reticulum.

Molecular cloning of human calmitine, a mitochondrial calcium binding protein, reveals identity with calsequestrine.

The cDNA of a mitochondrial calcium binding protein, "calmitine", has been cloned from a human skeletal muscle cDNA library. One cDNA of 1.8 kb has been isolated and sequenced. It encodes for a protein of 390 amino acid residues of 41,746 KDa and contains a leading peptide of 28 amino acids. The sequencing showed the possibility for 21 phosphorylation sites, 4 myristylation sites, and one N glycosylation site. Sequence comparison with other proteins revealed the identity of calmitine with calsequestrine, the sarcoplasmic reticulum low affinity, but high Ca2+ binding capacity, protein isolated in 1971. Subcellular fractionation showed a marked increase in these Ca2+ binding proteins in mitochondria as compared with the sarcoplasmic reticulum; furthermore the mitochondrial matrix is highly enriched with that protein. Therefore, our data either suggest a bicompartimentation of calmitine or indicate that the localization of calsequestrine should be reconsidered in the light of our data. Calmitine represents the Ca2+ reservoir of mitochondria, the function of which could be similar to what has been reported for calsequestrine in the sarcoplasmic reticulum.

Steady state levels of mitochondrial and nuclear oxidative phosphorylation transcripts in Kearns-Sayre syndrome.

The steady state levels of both mitochondrial and nuclear transcripts were examined in a Kearns-Sayre syndrome patient harboring a heteroplasmic 7.7 kb mitochondrial DNA deletion. Transcripts originating from the genes located outside of the deletion were present in similar amounts to those of control samples, with the transcript levels of each tissue linked to its oxidative phosphorylation capacities. Transcripts originating from genes within the deletion were reduced according to the percentage of mtDNA deleted molecules in the tissue. The fusion transcript resulting from the rearranged genome is expressed in all the tissues tested and its level is related to the amount of the deleted mtDNA. The RNA levels from three nuclear genes encoding two of the Adenine Nucleotide Translocator isoforms (ANT1 and 2) and the beta subunit of the ATPsynthase (ATPsyn beta) were significantly induced in the different tissues independently of the percentage of deleted mtDNA molecules. In contrast, the ANT1 and ATPsyn beta levels were decreased in skeletal muscle. This result could be related to the different distribution of the deleted molecules in tissues.

Mitochondrial DNA alterations and genetic diseases: a review.

We review the main features of human mitochondrial function and structure, and in particular mitochondrial transcription, translation, and replication cycles. Furthermore, some pecularities such as mitochondria's high polymorphism, the existence of mitochondrial pseudogenes, and the various considerations to take into account when studying mitochondrial diseases will also be mentioned. Mitochondrial syndromes mostly affecting the nervous system have, during the past few years, been associated with mitochondrial DNA (mt DNA) alterations such as deletions, duplications, mutations and depletions. We suggest a possible classification of mitochondrial diseases according to the kind of mt DNA mutations: structural mitochondrial gene mutation as in LHON (Leber's Hereditary Optic Neuropathy) and NARP (Neurogenic muscle weakness, Ataxia and Retinitis Pigmentosa) as well as some cases of Leigh's syndrome; transfer RNA and ribosomal RNA mitochondrial gene mutation as in MELAS (Mitochondrial Encephalomyopathy, Lactic Acidosis and Strokelike Episodes) or MERRF (Myoclonic Epilepsy with Ragged Red Fibers) or deafness with aminoglycoside; structural with transfer RNA mitochondrial gene mutations as observed in large-scale deletions or duplications in Kearns-Sayre syndrome, Pearson's syndrome, diabetes mellitus with deafness, and CPEO (Chronic Progressive External Ophtalmoplegia). Depletions of the mt DNA may also be classified in this category. Even though mutations are generally maternally inherited, most of the deletions are sporadic. However, multiple deletions or depletions may be transmitted in a mendelan trait which suggests that nuclear gene products play a primary role in these processes. The relationship between a mutation and a particular phenotype is far from being fully understood. Gene dosage and energic threshold, which are tissue-specific, appear to be the best indicators. However, the recessive or dominant behavior of both the wild type or the mutated genome appears to play a significant role, which can be verified with in vitro studies.

Juvenile Kearns-Sayre syndrome initially misdiagnosed as a psychosomatic disorder.

We have investigated a 15 year old girl with progressive external ophthalmoplegia, including bilateral ptosis and retinal rod and cone cell dysfunction with atypical retinal pigmentation, complicated by cerebellar ataxia, partial cardiac conduction block, and diabetes mellitus. In infancy she had a severe crisis of bone marrow depression, and as a child she suffered from hypersensitivity to light, increasing fatigue, and vertigo, signs that were initially though to be psychosomatic. Histological examination showed mitochondrial myopathy, and subsequent mitochondrial DNA (mtDNA) analysis showed a deletion of approximately 5500 base pairs in 35 to 40% of her muscle mtDNA. We therefore conclude that this patient has developed the Kearns-Sayre syndrome after a Pearson syndrome-like crisis in her first year of life.

Mitochondrial DNA expression in mitochondrial myopathies and coordinated expression of nuclear genes involved in ATP production.

The expression of nuclear and mitochondrial oxidative phosphorylation (OXPHOS) genes was examined in the skeletal muscle of patients with Kearns-Sayre syndrome (KSS), myoclonic epilepsy associated with ragged red fibers (MERRF), and myopathy, encephalopathy, lactic acidosis, and stroke-like episodes (MELAS) and compared with controls. In KSS muscle, mtDNA transcripts outside the deletion were elevated, while those within the deletion were reduced according to the percentage of deleted mtDNA molecules. In MERRF and MELAS muscle, mitochondrial transcripts levels were increased, but the increase was greater in MERRF muscle. The processing of mtDNA transcripts was reduced in all pathogenic muscles. This was true for full-length heavy and light strand transcripts as well as for the 16 S rRNA + tRNA(Leu)+ND1 transcript. However, the tRNA(Lys) level was reduced in all three muscles. In MELAS muscle, our results are not consistent with an impairment of transcription termination at the end of the 16 S mitochondrial rRNA. Finally, the transcription of the nuclear ATPsyn.beta and ANT1 genes was induced in parallel with the high level of mtDNA transcripts in MERRF and MELAS muscle, but was repressed in KSS muscle. The results demonstrate that the expression of nuclear and cytoplasmic OXPHOS genes is coordinated and that OXPHOS gene expression increases to compensate for respiratory deficiency. The repression of nuclear genes in KSS muscle could be a consequence of the segmental distribution of deleted mtDNA molecules in muscle cells.

Kearns-Sayre syndrome with sideroblastic anemia: molecular investigations.

The progressive syndrome of Kearns-Sayre has been studied at the clinical, biochemical and genetic levels in a patient. Clinical arguments suggest an evolution from Pearson's disease to Kearns-Sayre syndrome. The respiratory chain activities were low, and Southern blot analysis, together with gene sequencing, showed a heteroplasmic deletion of 7767 base pairs in a significant proportion of the mitochondrial DNA in different tissues. Protein synthesis studies on lymphoblasts did not reveal any translation of the new reading frame created by the deletion, although the corresponding deleted mitochondrial DNA sequence is transcribed.

Uneven distribution of mitochondrial DNA mutation in MERRF dizygotic twins.

A new family of myoclonic epilepsy with ragged-red fibers (MERRF) was studied at clinical, histological, biochemical and molecular genetic levels. There was a remarkable variation in the age of onset, the clinical presentation and the severity of symptoms. Multiple defects affecting respiratory chain complexes I, III and IV were detected in 2 patients. The point mutation at 8344 of the mitochondrial genome was found in all the maternal lineage with a relatively narrow range of variation in the percentage of mutant mitochondrial genomes. The one exception was represented by a set of dizygotic twins, one clinically affected and showing high proportions of mutant mitochondrial DNAs (mtDNAs) in blood cells, while the other was asymptomatic and showed very small amounts of mutant mt-DNAs in blood and skin. This could suggest an early segregation of the mitochondrial genome during ovogenesis.

Mitochondrial DNA mutations in human diseases: a review.

Human mitochondrial diseases have been associated recently with mitochondrial DNA mutations, duplications and deletions which impair the protein synthesis of the mitochondrial subunits of the respiratory chain complexes. A constant feature is the coincident presence of the mutated and wild type genomes which provide heteroplasmy. The clinical expression of these diseases depends on the relative expression of each kind of mitochondrial DNA in the various tissues, which in turn affects the production of ATP in these tissues. Research on nuclear gene products interfering with mtDNA or with its gene products is the next step towards understanding the etiology of these diseases.

Analysis of human mitochondrial transcripts using electron microscopic in situ hybridization.

Human mitochondrial transcripts have been examined at the ultrastructural level. After contact with ultrathin sections of a human lymphoid cell line (CEM) embedded in Lowicryl K4M, biotinylated mitochondrial probes yield specific hybrids identified by a colloidal gold immunocytochemistry marker that visualizes rRNA and mRNA coding for respiratory chain polypeptides CO II, CO III and ATPase-6. The mitochondrial transcripts are preferentially located close to the inner membrane, particularly the cristae, suggesting that intra-organelle protein synthesis is intimately associated with the mitochondrial membrane system. Quantitative analysis indicates that the mitochondria concentrate the labeling with intensities that vary with the type of RNA and that the nucleus induces a light hybridization signal with each mitochondrial probe. The visualization of human mitochondrial DNA expression in correlation with the fine anatomy of the mitochondria constitutes a new approach for fundamental research on the organelle and for analyzing its behaviour in human mitochondrial diseases.

Mutation detection in Leber's hereditary optic neuropathy by PCR with allele-specific priming.

An assay was designed that allows detection, by PCR alone, of the mutation of base pair no. 11,778 in human mitochondrial DNA, causing Leber's hereditary optic neuropathy. This was obtained by using a 20-mer primer with the mutation-specific base in the 3'-position, plus a deliberately introduced C/C-mismatch at base no. four from the 3'-end. The latter mismatch was necessary, and sufficient, to prevent amplification of the normal allele.